StartracDiversity: Startrac-based diversity indices for single-cell RNA-seq

In ncborcherding/scRepertoire: A toolkit for single-cell immune receptor profiling

Startrac-based diversity indices for single-cell RNA-seq

Description

This function utilizes the Startrac approach derived from PMID: 30479382. Required to run the function, the "type" variable needs to include the difference in where the cells were derived. The output of this function will produce 3 indices: expa (clonal expansion), migra (cross-tissue migration), and trans (state transition). In order to understand the underlying analyses of the outputs please read and cite the linked manuscript.

Usage

StartracDiversity(
  sc.data,
  cloneCall = "strict",
  chain = "both",
  type = NULL,
  group.by = NULL,
  exportTable = FALSE,
  palette = "inferno"
)

Arguments

sc.data	The single-cell object after combineExpression(). For SCE objects, the cluster variable must be in the meta data under "cluster".
cloneCall	How to call the clone - VDJC gene (gene), CDR3 nucleotide (nt), CDR3 amino acid (aa), VDJC gene + CDR3 nucleotide (strict) or a custom variable in the data.
chain	indicate if both or a specific chain should be used - e.g. "both", "TRA", "TRG", "IGH", "IGL".
type	The variable in the meta data that provides tissue type.
group.by	The variable in the meta data to group by, often samples.
exportTable	Returns the data frame used for forming the graph.
palette	Colors to use in visualization - input any hcl.pals.

Value

ggplot object of Startrac diversity metrics

Author(s)

Liangtao Zheng

Examples

#Getting the combined contigs
combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))

#Getting a sample of a Seurat object
scRep_example  <- get(data("scRep_example"))
scRep_example  <- combineExpression(combined, scRep_example)
scRep_example$Patient <- substring(scRep_example$orig.ident,1,3)
scRep_example$Type <- substring(scRep_example$orig.ident,4,4) 

#Using StartracDiversity()
StartracDiversity(scRep_example, 
                  type = "Type", 
                  group.by = "Patient")

ncborcherding/scRepertoire documentation built on Nov. 5, 2024, 2:05 p.m.